The directory structures are mirrored between local and remote installations, so C:\Program Files (x86)\BigFix Enterprise\BES Server\WebUI becomes C:\Program Files (x86)\BigFix Enterprise\BES WebUI\WebUI
The instructions are as I mentioned earlier in this post:
If you have done this, and it isn’t working, then your files are not properly formatted or do not contain the proper data. Based on the file list you posted, you will need to open your .crt files in notepad or some other text editor, and copy the intermediate certs and root cert below the server cert, so they are all in one file. Make sure you include all the --------BEGIN CERTIFICATE----------- and -----------END CERTIFICATE----------- headers/footers just as they are in each cert.
The one thing I don’t see is your .key or .pvk file. It is probably included in your .p7b file, and will have to be extracted using OpenSSL or something similar.